Pyrazinamide-resistant Tuberculosis Obscured From Common Targeted Molecular Diagnostics.

Autor: Modlin SJ; Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, School of Public Health, San Diego State University, San Diego, CA, USA., Mansjö M; Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden., Werngren J; Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden., Ejike CM; Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, School of Public Health, San Diego State University, San Diego, CA, USA., Hoffner SE; Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, School of Public Health, San Diego State University, San Diego, CA, USA; Department of Global Public Health, Karolinska Institute, Stockholm, Sweden., Valafar F; Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, School of Public Health, San Diego State University, San Diego, CA, USA. Electronic address: faramarz@sdsu.edu.
Jazyk: angličtina
Zdroj: Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy [Drug Resist Updat] 2023 May; Vol. 68, pp. 100959. Date of Electronic Publication: 2023 Apr 06.
DOI: 10.1016/j.drup.2023.100959
Abstrakt: Here, we describe a clinical case of pyrazinamide-resistant (PZA-R) tuberculosis (TB) reported as PZA-susceptible (PZA-S) by common molecular diagnostics. Phenotypic susceptibility testing (pDST) indicated PZA-R TB. Targeted Sanger sequencing reported wild-type PncA, indicating PZA-S TB. Whole Genome Sequencing (WGS) by PacBio and IonTorrent both detected deletion of a large portion of pncA, indicating PZA-R. Importantly, both WGS methods showed deletion of part of the primer region targeted by Sanger sequencing. Repeating Sanger sequencing from a culture in presence of PZA returned no result, revealing that 1) two minority susceptible subpopulations had vanished, 2) the PZA-R majority subpopulation harboring the pncA deletion could not be amplified by Sanger primers, and was thus obscured by amplification process. This case demonstrates how a small susceptible subpopulation can entirely obscure majority resistant populations from targeted molecular diagnostics and falsely imply homogenous susceptibility, leading to incorrect diagnosis. To our knowledge, this is the first report of a minority susceptible subpopulation masking a majority resistant population, causing targeted molecular diagnostics to call false susceptibility. The consequence of such genomic events is not limited to PZA. This phenomenon can impact molecular diagnostics' sensitivity whenever the resistance-conferring mutation is not fully within primer-targeted regions. This can be caused by structural changes of genomic context with phenotypic consequence as we report here, or by uncommon mechanisms of resistance. Such false susceptibility calls promote suboptimal treatment and spread of strains that challenge targeted molecular diagnostics. This motivates development of molecular diagnostics unreliant on primer conservation, and impels frequent WGS surveillance for variants that evade prevailing molecular diagnostics.
Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)
Databáze: MEDLINE
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